def testSubTreesConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'node508'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'ingroup'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
def testTreesCulledNonmatcingConvViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='1.2.1', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
rx = json.loads(x)
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testTreesCulledNonmatcingConvViaPSV0(self):
"""Verify that the culling does not break the conversion to other forms of NexSON"""
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='0.0.0', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
rx = json.loads(x)
self.assertEqual(detect_nexson_version(rx), '0.0.0')
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testNexmlConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nexml', otu_label='otttaxonname')
nex = ps.serialize(o, src_schema=PhyloSchema('nexson', version='1.2.1'))
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def testNewickConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNexusConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(None, type_ext='.nex', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexmlConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexml')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def testOtuMapConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexson', content='otumap', version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
def testOtuMapConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexson', content='otumap', version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('{')) #pylint: disable=E1103
def testNewickConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('(')) #pylint: disable=E1103
def testNexmlConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexml')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('<')) #pylint: disable=E1103
def testNexmlConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nexml', otu_label='otttaxonname')
nex = ps.serialize(o,
src_schema=PhyloSchema('nexson', version='1.2.1'))
self.assertTrue(nex.startswith('<')) #pylint: disable=E1103
